TElocal: a tool that utilizes both uniquely and ambiguously mapped reads to quantify transposable element expression at the locus level.

TElocal: a tool that utilizes both uniquely and ambiguously mapped reads to quantify transposable element expression at the locus level.

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

[user@biowulf]$ sinteractive  
[user@cn0861 ~]$ module load TElocal 
[+] Loading singularity  3.8.5-1  on cn4177
[+] Loading TElocal 1.1.2  ...
[user@cn0861 ~]$ TElocal -h 
usage: TElocal [-h] -b RNAseq.bam --GTF genic-GTF-file --TE TE-annot-file [--stranded option] [--mode TE counting mode]
               [--project name] [--sortByPos] [-i iteration] [--maxL maxL] [--minL minL] [-L fragLength]
               [--verbose [verbose]] [--version]

Measuring TE expression per-locus, per-sample.

optional arguments:
  -h, --help            show this help message and exit
  -b RNAseq.bam, --BAM RNAseq.bam
                        An RNAseq BAM file.
  --GTF genic-GTF-file  GTF or db file for gene annotations
  --TE TE-annot-file    locInd file for transposable element annotations
  --stranded option     Is this a stranded library? (forward, no, or reverse). For "first-strand" cDNA libraries (e.g.
                        TruSeq), choose reverse. For "second-strand" cDNA libraries (e.g. QIAseq stranded), choose
                        forward. DEFAULT: no.
  --mode TE counting mode
                        How to count TE: uniq (unique mappers only), or multi (distribute among all alignments).
                        DEFAULT: multi
  --project name        Name of this project. DEFAULT: TElocal_out
  --sortByPos           Alignment file is sorted by chromosome position.
  -i iteration, --iteration iteration
                        number of iteration to run the optimization. DEFAULT: 100
  --maxL maxL           maximum fragment length. DEFAULT:500
  --minL minL           minimum fragment length. DEFAULT:0
  -L fragLength, --fragmentLength fragLength
                        average fragment length for single end reads. For paired-end, estimated from the input alignment
                        file. DEFAULT: for paired-end, estimate from the input alignment file; for single-end, ignored
                        by default.
  --verbose [verbose]   Set verbose level. 0: only show critical message, 1: show additional warning message, 2: show
                        process information, 3: show debug messages. DEFAULT:2
  --version             show program's version number and exit

Example: TElocal -b RNAseq.bam --GTF gene_annotation.gtf --TE TE_annotation.locInd --mode multi

etc.
[user@cn0861 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226